To understand the various players that drive cell differentiation, i.e., cell-cell communication, gene regulation and interactions with other processes such as proliferation, we require an integrated systems approach that looks at all these facets together. While current models focus on only one of the components, in the ChromaConnect project I will create a model that uses single-nucleus RNA+ATAC data to connect these different layers within a unified modelling framework. I will apply this framework to study in vivo Kupffer cell differentiation. Using the multiplexed genetic manipulation tools established in the lab, 100 receptors and transcription factors will be validated at the phenotypic level in vivo. Next, 20 factors will be further studied at the single-cell RNA-seq level and analyzed using the same computational framework, which will provide both validation and greatly improve our understanding of how these factors are integrated on the genome. Finally, I will use an experiment-in-the-loop approach to identify the gaps in the framework and provide solutions by integrating possible extra data sources. Overall, this project will not only provide an unprecedented “molecule”-wide look at KC differentiation but will also provide a showcase on whether similar analyses can be performed on other case studies in cancer or inflammation.